A Taiwanese fishing boat was seized by Japan's Fisheries Agency in waters near Taketomi island on Monday. Photo: AFP

Japan seized a Taiwanese fishing boat inside its exclusive economic zone on Tuesday, the first incident since Tokyo and Taipei signed a fishing rights accord for disputed waters, the Fisheries Agency said.

The Taiwanese fishing boat was spotted in waters near Taketomi island, part of Japan’s southern Okinawa chain, the agency said.

One of the agency’s patrol ships seized the boat and arrested the captain, it said.

The incident occurred outside the waters that are at the centre of a three-way territorial tussle involving Taipei, Tokyo and Beijing for which Japan and Taiwan have agreed fishing rights.

Under the agreement, Taiwanese trawlers are permitted to fish in waters off East China Sea islands controlled by Japan as the Senkakus, but also claimed by China and Taiwan as the Diaoyus.